Unsupported HDF5 version

[sidec]

It seems that HDF5 version: 1.10.0 is not supported.

/home/przemek/torch/install/bin/luajit: /home/przemek/torch/install/share/lua/5.1/trepl/init.lua:383: /home/przemek/torch/install/share/lua/5.1/trepl/init.lua:383: /home/przemek/torch/install/share/lua/5.1/hdf5/ffi.lua:71: Unsupported HDF5 version: 1.10.0
stack traceback:
    [C]: in function 'error'
    /home/przemek/torch/install/share/lua/5.1/trepl/init.lua:383: in function 'require'
    train.lua:6: in main chunk
    [C]: in function 'dofile'
    ...emek/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:145: in main chunk
    [C]: at 0x00405be0

Is there any workaround for non-root user on Linux?

[MrKroo]

On mac right?

[ghost]

I'm in fact experiencing the same on arch linux (after indeed updating the hdf5 library) To be fair due to time limitations and deadlines I just installed ubuntu on a drive and went on with that (where it still seems to work).

I have the feeling like one of the lua libraries should simply be updated (but I haven't figured out which one) (I'm very new to the lua language)

[MrKroo]

I fixed my issue on mac by installing hdf5 with homebrew and uninstalling it on MacPorts as it was using a more recent version (1.10). After this I ran the script bash install-deps and ./install.sh and everything built without error.

[chrbauer]

Some advice for Arch Linux 64bit and hdf5:

There is a package hdf5_18. I installed this package and updated torch/install/share/lua/5.1/hdf5/config.lua

 HDF5_LIBRARIES = "/usr/lib/hdf5_18/libhdf5.so"

Next problem is the assert in file.lua. fileID has the type "cdata" instead of number (because it's 64bit). I simply changed the check in the assert.

Last problem is in group.lua. Also the groupID is an int64-cdata. It works for me, if I convert the groupID in line 37 to a number: self._groupID = tonumber(groupID)

[bluetyson]

Thanks for that!

[mendadala]

Please help! I am using Mac with Yosemite 10.10.5 with CUDA 7.5 and followed ("https://www.jeffreythompson.org/blog/2016/03/25/torch-rnn-mac-install/") to install torch. Here it states installing HDF5 using homebrew: brew tap homebrew/science brew install hdf5 Getting same error!

Rajas-MBP:torch-rnn neptune$ th train.lua -input_h5 data/tiny_shakespeare.h5 -input_json data/tiny_shakespeare.json /Users/neptune/torch/install/bin/luajit: /Users/neptune/torch/install/share/lua/5.1/trepl/init.lua:389: /Users/neptune/torch/install/share/lua/5.1/trepl/init.lua:389: /Users/neptune/torch/install/share/lua/5.1/hdf5/ffi.lua:42: Error: unable to locate HDF5 header file at /usr/local/Cellar/hdf5/1.10.1_2/include;/usr/local/opt/szip/include/hdf5.h stack traceback: [C]: in function 'error' /Users/neptune/torch/install/share/lua/5.1/trepl/init.lua:389: in function 'require' train.lua:6: in main chunk [C]: in function 'dofile' ...tune/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk [C]: at 0x0102588bd0

[MelomanCool]

There is a fork of torch-hdf5 that supports 1.10: https://github.com/anibali/torch-hdf5. Also, there is a pull request for torch-rnn which uses that fork: #215

The fix is pretty simple (copied from #215's readme):

git clone https://github.com/anibali/torch-hdf5.git
cd torch-hdf5
git checkout hdf5-1.10 
luarocks make hdf5-0-0.rockspec

[agilebean]

Alternatively to the correct solution given by @MelomanCool, you can install the correct hdf5 bindings directly via luarocks:

luarocks install https://raw.githubusercontent.com/deepmind/torch-hdf5/master/hdf5-0-0.rockspec